› 4v4w

Electron Microscopy
15Å resolution

Structure of a SecM-stalled E. coli ribosome complex obtained by fitting atomic models for RNA and protein components into cryo-EM map EMD-1143

Released:
DOI: 10.2210/pdb4v4w/pdb
PDB entry 4v4w coloured by chain, front view.
PDB entry 4v4w coloured by chain, side view.
PDB entry 4v4w coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Elongation arrest by SecM via a cascade of ribosomal RNA rearrangements.
Mitra K, Schaffitzel C, Fabiola F, Chapman MS, Ban N, Frank J
Mol Cell 22 533-43 (2006)
PMID: 16713583
Related structures: EMD-1143

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 52-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-135579 (preferred)
Entry contents:
45 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (49 distinct):
Small ribosomal subunit protein uS2 Chain: AB
Molecule details ›
Chain: AB
Length: 236 amino acids
Theoretical weight: 26.29 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7V0 (Residues: 6-241; Coverage: 98%)
Gene names: JW0164, b0169, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chain: AC
Molecule details ›
Chain: AC
Length: 206 amino acids
Theoretical weight: 23.08 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7V3 (Residues: 2-207; Coverage: 88%)
Gene names: JW3276, b3314, rpsC
Sequence domains:
Small ribosomal subunit protein uS4 Chain: AD
Molecule details ›
Chain: AD
Length: 204 amino acids
Theoretical weight: 23.31 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7V8 (Residues: 3-206; Coverage: 99%)
Gene names: JW3258, b3296, ramA, rpsD
Sequence domains:
Small ribosomal subunit protein uS5 Chain: AE
Molecule details ›
Chain: AE
Length: 148 amino acids
Theoretical weight: 15.62 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7W1 (Residues: 10-157; Coverage: 89%)
Gene names: JW3265, b3303, rpsE, spc
Sequence domains:
Small ribosomal subunit protein bS6, non-modified isoform Chain: AF
Molecule details ›
Chain: AF
Length: 95 amino acids
Theoretical weight: 11.18 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P02358 (Residues: 1-95; Coverage: 70%)
Gene names: JW4158, b4200, rpsF
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS7 Chain: AG
Molecule details ›
Chain: AG
Length: 137 amino acids
Theoretical weight: 15.38 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P02359 (Residues: 20-156; Coverage: 77%)
Gene names: JW3303, b3341, rpsG
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS8 Chain: AH
Molecule details ›
Chain: AH
Length: 127 amino acids
Theoretical weight: 13.86 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7W7 (Residues: 3-129; Coverage: 98%)
Gene names: JW3268, b3306, rpsH
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS9 Chain: AI
Molecule details ›
Chain: AI
Length: 126 amino acids
Theoretical weight: 14.44 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7X3 (Residues: 5-130; Coverage: 97%)
Gene names: JW3199, b3230, rpsI
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10 Chain: AJ
Molecule details ›
Chain: AJ
Length: 96 amino acids
Theoretical weight: 11 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7R5 (Residues: 5-100; Coverage: 93%)
Gene names: JW3283, b3321, nusE, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11 Chain: AK
Molecule details ›
Chain: AK
Length: 116 amino acids
Theoretical weight: 12.39 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7R9 (Residues: 13-128; Coverage: 90%)
Gene names: JW3259, b3297, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chain: AL
Molecule details ›
Chain: AL
Length: 101 amino acids
Theoretical weight: 11.25 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7S3 (Residues: 23-123; Coverage: 82%)
Gene names: JW3304, b3342, rpsL, strA
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13 Chain: AM
Molecule details ›
Chain: AM
Length: 115 amino acids
Theoretical weight: 12.74 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7S9 (Residues: 2-116; Coverage: 98%)
Gene names: JW3260, b3298, rpsM
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS14 Chain: AN
Molecule details ›
Chain: AN
Length: 61 amino acids
Theoretical weight: 7.12 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0AG59 (Residues: 41-101; Coverage: 60%)
Gene names: JW3269, b3307, rpsN
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS15 Chain: AO
Molecule details ›
Chain: AO
Length: 86 amino acids
Theoretical weight: 9.92 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0ADZ4 (Residues: 3-88; Coverage: 97%)
Gene names: JW3134, b3165, rpsO, secC
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16 Chain: AP
Molecule details ›
Chain: AP
Length: 78 amino acids
Theoretical weight: 8.82 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7T3 (Residues: 1-78; Coverage: 95%)
Gene names: JW2590, b2609, rpsP
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein uS17 Chain: AQ
Molecule details ›
Chain: AQ
Length: 79 amino acids
Theoretical weight: 9.13 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0AG63 (Residues: 6-84; Coverage: 94%)
Gene names: JW3273, b3311, neaA, rpsQ
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein bS18 Chain: AR
Molecule details ›
Chain: AR
Length: 69 amino acids
Theoretical weight: 8.18 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7T7 (Residues: 7-75; Coverage: 92%)
Gene names: JW4160, b4202, rpsR
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein uS19 Chain: AS
Molecule details ›
Chain: AS
Length: 87 amino acids
Theoretical weight: 9.87 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7U3 (Residues: 2-88; Coverage: 95%)
Gene names: JW3278, b3316, rpsS
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein bS20 Chain: AT
Molecule details ›
Chain: AT
Length: 83 amino acids
Theoretical weight: 9.28 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7U7 (Residues: 5-87; Coverage: 95%)
Gene names: JW0022, b0023, rpsT
Sequence domains: Ribosomal protein S20
Large ribosomal subunit protein uL1 Chain: B2
Molecule details ›
Chain: B2
Length: 222 amino acids
Theoretical weight: 23.59 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7L0 (Residues: 6-227; Coverage: 95%)
Gene names: JW3947, b3984, rplA
Sequence domains: Ribosomal protein L1p/L10e family
Large ribosomal subunit protein bL12 Chains: B3, B5
Molecule details ›
Chains: B3, B5
Length: 119 amino acids
Theoretical weight: 12.09 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7K2 (Residues: 3-121; Coverage: 98%)
Gene names: JW3949, b3986, rplL
Sequence domains:
Large ribosomal subunit protein uL2 Chain: BA
Molecule details ›
Chain: BA
Length: 227 amino acids
Theoretical weight: 24.69 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P60422 (Residues: 39-265; Coverage: 83%)
Gene names: JW3279, b3317, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chain: BB
Molecule details ›
Chain: BB
Length: 209 amino acids
Theoretical weight: 22.28 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P60438 (Residues: 1-209; Coverage: 100%)
Gene names: JW3282, b3320, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chain: BC
Molecule details ›
Chain: BC
Length: 198 amino acids
Theoretical weight: 21.81 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P60723 (Residues: 1-198; Coverage: 99%)
Gene names: JW3281, b3319, eryA, rplD
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5 Chain: BD
Molecule details ›
Chain: BD
Length: 177 amino acids
Theoretical weight: 20.13 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P62399 (Residues: 3-179; Coverage: 99%)
Gene names: JW3270, b3308, rplE
Sequence domains:
Large ribosomal subunit protein uL6 Chain: BE
Molecule details ›
Chain: BE
Length: 167 amino acids
Theoretical weight: 17.8 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0AG55 (Residues: 6-172; Coverage: 94%)
Gene names: JW3267, b3305, rplF
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein bL9 Chain: BF
Molecule details ›
Chain: BF
Length: 149 amino acids
Theoretical weight: 15.79 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7R1 (Residues: 1-149; Coverage: 100%)
Gene names: JW4161, b4203, rplI
Sequence domains:
Large ribosomal subunit protein uL11 Chain: BG
Molecule details ›
Chain: BG
Length: 139 amino acids
Theoretical weight: 14.58 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7J7 (Residues: 3-141; Coverage: 98%)
Gene names: JW3946, b3983, relC, rplK
Sequence domains:
Large ribosomal subunit protein uL13 Chain: BH
Molecule details ›
Chain: BH
Length: 142 amino acids
Theoretical weight: 16.05 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0AA10 (Residues: 1-142; Coverage: 100%)
Gene names: JW3200, b3231, rplM
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14 Chain: BI
Molecule details ›
Chain: BI
Length: 122 amino acids
Theoretical weight: 13.43 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0ADY3 (Residues: 2-123; Coverage: 99%)
Gene names: JW3272, b3310, rplN
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL15 Chain: BJ
Molecule details ›
Chain: BJ
Length: 140 amino acids
Theoretical weight: 14.48 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P02413 (Residues: 4-143; Coverage: 97%)
Gene names: JW3263, b3301, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16 Chain: BK
Molecule details ›
Chain: BK
Length: 131 amino acids
Theoretical weight: 14.74 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0ADY7 (Residues: 3-133; Coverage: 96%)
Gene names: JW3275, b3313, rplP
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein bL17 Chain: BL
Molecule details ›
Chain: BL
Length: 114 amino acids
Theoretical weight: 12.95 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0AG44 (Residues: 3-116; Coverage: 90%)
Gene names: JW3256, b3294, rplQ
Sequence domains: Ribosomal protein L17
Large ribosomal subunit protein uL18 Chain: BM
Molecule details ›
Chain: BM
Length: 113 amino acids
Theoretical weight: 12.27 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0C018 (Residues: 3-115; Coverage: 97%)
Gene names: JW3266, b3304, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Large ribosomal subunit protein bL19 Chain: BN
Molecule details ›
Chain: BN
Length: 114 amino acids
Theoretical weight: 13.03 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7K6 (Residues: 2-115; Coverage: 99%)
Gene names: JW2587, b2606, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20 Chain: BO
Molecule details ›
Chain: BO
Length: 115 amino acids
Theoretical weight: 13.25 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7L3 (Residues: 3-117; Coverage: 98%)
Gene names: JW1706, b1716, pdzA, rplT
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein uL22 Chain: BQ
Molecule details ›
Chain: BQ
Length: 106 amino acids
Theoretical weight: 11.78 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P61175 (Residues: 5-110; Coverage: 96%)
Gene names: JW3277, b3315, eryB, rplV
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23 Chain: BR
Molecule details ›
Chain: BR
Length: 92 amino acids
Theoretical weight: 10.21 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0ADZ0 (Residues: 7-98; Coverage: 92%)
Gene names: JW3280, b3318, rplW
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24 Chain: BS
Molecule details ›
Chain: BS
Length: 99 amino acids
Theoretical weight: 10.82 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P60624 (Residues: 4-102; Coverage: 95%)
Gene names: JW3271, b3309, rplX
Sequence domains:
Large ribosomal subunit protein bL25 Chain: BT
Molecule details ›
Chain: BT
Length: 94 amino acids
Theoretical weight: 10.71 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P68919 (Residues: 1-94; Coverage: 100%)
Gene names: JW2173, b2185, rplY
Sequence domains: Ribosomal L25p family
Large ribosomal subunit protein bL27 Chain: BU
Molecule details ›
Chain: BU
Length: 84 amino acids
Theoretical weight: 9.02 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7L8 (Residues: 2-85; Coverage: 99%)
Gene names: JW3152, b3185, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein uL29 Chain: BW
Molecule details ›
Chain: BW
Length: 60 amino acids
Theoretical weight: 7.09 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7M6 (Residues: 1-60; Coverage: 95%)
Gene names: JW3274, b3312, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chain: BX
Molecule details ›
Chain: BX
Length: 56 amino acids
Theoretical weight: 6.22 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0AG51 (Residues: 4-59; Coverage: 95%)
Gene names: JW3264, b3302, rpmD
Sequence domains: Ribosomal protein L30p/L7e
Large ribosomal subunit protein bL32 Chain: BZ
Molecule details ›
Chain: BZ
Length: 29 amino acids
Theoretical weight: 3.32 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7N4 (Residues: 28-56; Coverage: 51%)
Gene names: JW1075, b1089, rpmF
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL33 Chain: B1
Molecule details ›
Chain: B1
Length: 52 amino acids
Theoretical weight: 6.02 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7N9 (Residues: 2-53; Coverage: 95%)
Gene names: JW3611, b3636, rpmG
Sequence domains: Ribosomal protein L33
16S ribosomal RNA Chain: AA
Molecule details ›
Chain: AA
Length: 1488 nucleotides
Theoretical weight: 482.29 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
tRNA Chains: AU, AV, AW
Molecule details ›
Chains: AU, AV, AW
Length: 76 nucleotides
Theoretical weight: 24.52 KDa
Sequence domains: tRNA
23S ribosomal RNA Chain: B0
Molecule details ›
Chain: B0
Length: 2740 nucleotides
Theoretical weight: 888.5 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: B9
Molecule details ›
Chain: B9
Length: 108 nucleotides
Theoretical weight: 34.92 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 15Å
Relevant EMDB volumes: EMD-1143

Quick links

Citations

15 review citations

Protein translocation across the eukaryotic endoplasmic reticulum and bacterial plasma membranes.
Rapoport TA. (2007)
14 more

2 mentions without citation

Rapid automated superposition of shapes and macromolecular models using spherical harmonics.
Konarev et al. (2016)
1 more